Sun Oct 9 11:16:53 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 11:16:53 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2848 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6234349 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -22.57100 34.53200 ymin,ymax (A): -25.31600 26.09500 zmin,zma (A): -30.87400 25.93500 x,y,z range (A): 57.10300 51.41100 56.80900 scale (grids/A): 0.6234349 object centre (A): 5.980498 0.3894997 -2.469501 number of atom coordinates read : 2848 total number of charged atoms : 2760 net assigned charge : 5.000010 assigned positive charge : 420.9171 centred at (gu) : 90.70983 90.37560 92.13114 assigned negative charge : -415.9188 centred at (gu) : 90.71225 90.33568 92.08023 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7794 nv = 96 ne = 84 npr = 54904 no. pairs analyzed = 54904 no. exposed pairs = 3973 no. arc points = 28058 no. surface atoms = 1324 nbur = 1524 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 471 mr = 3984 m= 3 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 4234 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2697 ## 206 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 9303 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.7618757E-10 1.3259873E-08 midg,1,midg; midg,igrid,midg 1.1212705E-09 8.0774614E-09 1,midg,midg; igrid,midg,midg 3.8961741E-09 4.8196065E-09 gauss-seidel spectral radius is 0.9867147 estimated iterations to convergence 71 setup time was (sec) 0.4200000 now iterating at: 11:16:54 rms-change max change #iterations 0.1360985 20.22693 at 10iterations 1.2999161E-02 1.815889 at 20iterations 1.3494821E-03 0.1860008 at 30iterations 2.1624719E-04 3.4337044E-02 at 40iterations 5.1626699E-05 8.8939667E-03 at 50iterations finished qdiffx linear iterations at : 11:16:56 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 5.1626699E-05 8.8939667E-03 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.500000 DelPhi exited at 11:16:57 3.501u 0.157s 0:04.08 89.4% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 11:16:57 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2848 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.870305 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -22.57100 34.53200 ymin,ymax (A): -25.31600 26.09500 zmin,zma (A): -30.87400 25.93500 x,y,z range (A): 57.10300 51.41100 56.80900 scale (grids/A): 1.870305 object centre (A): 5.980498 0.3894997 -2.469501 number of atom coordinates read : 2848 total number of charged atoms : 2760 net assigned charge : 5.000010 assigned positive charge : 420.9171 centred at (gu) : 92.12829 91.12591 96.39237 assigned negative charge : -415.9188 centred at (gu) : 92.13666 91.00697 96.24065 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 83444 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28058 grid for indexing accessible points = 1.400000 m= 30064 mr = 55373 m= 5212 mr = 21379 m= 301 mr = 3194 m= 3 mr = 90 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 502 time to turn everything in is 0.4000000 number of dielectric boundary points 38988 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 124 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 21661 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.6234349 object centre at (A) : 5.980498 0.3894997 -2.469501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0962518E-03 2.2171386E-02 midg,1,midg; midg,igrid,midg 2.5701119E-02 3.2381915E-02 1,midg,midg; igrid,midg,midg 1.0539539E-02 -2.5682332E-02 gauss-seidel spectral radius is 0.9986370 estimated iterations to convergence 215 setup time was (sec) 0.6300000 now iterating at: 11:16:58 rms-change max change #iterations 4.279623 181.9125 at 10iterations 1.997714 75.70901 at 20iterations 0.9338497 31.52740 at 30iterations 0.4363594 13.52022 at 40iterations 0.2041037 6.504956 at 50iterations 9.5649242E-02 2.906435 at 60iterations 4.4871155E-02 1.446356 at 70iterations 2.0973299E-02 0.6466064 at 80iterations 9.8351659E-03 0.3088284 at 90iterations 4.6456447E-03 0.1543579 at 100iterations 2.1886437E-03 8.0379486E-02 at 110iterations 1.0358157E-03 3.1774759E-02 at 120iterations finished qdiffx linear iterations at : 11:17:05 total time elapsed so far: 7.860000 # loops : 120 mean,max change (kT/e) : 1.0358157E-03 3.1774759E-02 energy calculations done at 7.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.000000 DelPhi exited at 11:17:06 8.000u 0.202s 0:08.53 96.1% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 11:17:06 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2848 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.805457 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -22.57100 34.53200 ymin,ymax (A): -25.31600 26.09500 zmin,zma (A): -30.87400 25.93500 x,y,z range (A): 57.10300 51.41100 56.80900 scale (grids/A): 2.805457 object centre (A): 5.980498 0.3894997 -2.469501 number of atom coordinates read : 2848 total number of charged atoms : 2760 net assigned charge : 5.000010 assigned positive charge : 420.9171 centred at (gu) : 93.19214 91.68871 99.58836 assigned negative charge : -415.9188 centred at (gu) : 93.20493 91.51032 99.36082 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 192653 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28058 grid for indexing accessible points = 1.400000 m= 95344 mr = 135240 m= 36317 mr = 75578 m= 9397 mr = 28572 m= 1321 mr = 6846 m= 57 mr = 801 m= 0 mr = 13 time to grow re-entrant surface = 0.6200000 no. cavity mid-points inaccessible to solvent = 1865 time to turn everything in is 1.060000 number of dielectric boundary points 88039 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.160000 number of grid points assigned charge 22072 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.870305 object centre at (A) : 5.980498 0.3894997 -2.469501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.6355872E-02 0.1786253 midg,1,midg; midg,igrid,midg 0.3817950 0.3658260 1,midg,midg; igrid,midg,midg 0.1543017 -0.4253552 gauss-seidel spectral radius is 0.9992818 estimated iterations to convergence 294 setup time was (sec) 1.310000 now iterating at: 11:17:07 rms-change max change #iterations 10.28792 293.4017 at 10iterations 6.159050 127.0420 at 20iterations 3.635584 78.74819 at 30iterations 2.142494 47.52072 at 40iterations 1.260249 25.53820 at 50iterations 0.7369916 13.90889 at 60iterations 0.4298023 8.167389 at 70iterations 0.2504772 4.277485 at 80iterations 0.1457230 2.447573 at 90iterations 8.4587909E-02 1.525192 at 100iterations 4.9256723E-02 0.9405766 at 110iterations 2.8601069E-02 0.5842314 at 120iterations 1.6619768E-02 0.3062037 at 130iterations 9.6593034E-03 0.1777191 at 140iterations 5.6209685E-03 9.4218493E-02 at 150iterations 3.2767574E-03 5.8256626E-02 at 160iterations 1.9145377E-03 3.6302805E-02 at 170iterations 1.1261165E-03 1.9638062E-02 at 180iterations finished qdiffx linear iterations at : 11:17:19 total time elapsed so far: 12.86000 # loops : 180 mean,max change (kT/e) : 1.1261165E-03 1.9638062E-02 energy calculations done at 12.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.00000 DelPhi exited at 11:17:19 13.005u 0.208s 0:13.55 97.4% 0+0k 0+0io 0pf+0w